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TODO comments for Eric

This commit is contained in:
Mark DePristo 2011-08-04 18:07:50 -04:00
parent 58a60d4901
commit 9be1ee59cc
1 changed files with 16 additions and 0 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -231,6 +231,22 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
for ( String sampleName : sampleNamesForStratification ) {
VariantContext eval = vcs.containsKey(evalName) && vcs.get(evalName) != null ? vcs.get(evalName).get(sampleName) : null;
// todo: Eric, this is really the problem. We select single eval and comp VCs independently
// todo: discarding multiple eval tracks at the sites and not providing matched comps
// todo: where appropriate. Really this loop should look like:
// todo: for each eval track:
// todo: for each eval in track:
// todo: for each compTrack:
// todo: comp = findMatchingComp(eval, compTrack) // find the matching comp in compTrack
// todo: call evalModule(eval, comp)
// todo: // may return null if no such comp exists, but proceed as eval modules may need to see eval / null pair
// todo: for each comp not matched by an eval in compTrack:
// todo: call evalModule(null, comp)
// todo: // need to call with null comp, as module
// todo: note that the reason Kiran pre-computed the possible VCs is to apply the modifiers
// todo: like subset to sample, etc. So you probably will want a master map that maps
// todo: from special eval bindings to the digested VC for efficiency.
if ( typesToUse != null ) {
if ( eval != null && ! typesToUse.contains(eval.getType()) ) eval = null;
if ( comp != null && ! typesToUse.contains(comp.getType()) ) comp = null;